That all changed in December 1979, when the Soviet Union invaded neighboring Afghanistan, driving hundreds of thousands of Afghan refugees—mainly conservative Pashtun tribesmen—across the border into Pakistan. Within months Zia's Islamist dream got a huge boost: The United States and Saudi Arabia joined Pakistan in a covert alliance to supply arms, training, and billions of dollars to an anti-Soviet insurgency in Afghanistan. The motto of Zia's army—Jihad in the Service of Allah—became a rallying cry for thousands of mujahideen training in camps funded by the CIA in Pakistan's North-West Frontier Province. Over time, Zia's agenda, and that of the United States, became indistinguishable: If Zia wanted to Islamize Pakistan while mobilizing support for the anti-Soviet jihad, all the more power to him. Besides, the fundamentalist madrassas of northwestern Pakistan made excellent recruiting centers for mujahideen—young fighters who saw the struggle against the Soviets as a holy war.

During the 1980s, as the mujahideen prevailed against the Soviets in Afghanistan, the winds of extremism blowing from the northwest began to chill all of Pakistan. Millions of dollars from Saudi Arabia flowed into the hard-line Sunni madrassas clustered along Pakistan's border with Afghanistan, which eventually spread across Pakistan. Not all Pakistani madrassas today are fundamentalist or radical. Some are shoestring operations run by moderate clerics to meet the educational needs of the poor. But the majority—more than 60 percent—are affiliated with the fundamentalist Deobandi sect, an austere interpretation of Islam that calls for a rejection of modernity and a return to the "pure," seventh-century Islam of the Prophet Muhammad. Politically savvy and extremely well funded, more than 10,000 of these schools operate across Pakistan today, compared with fewer than 1,000 before General Zia took power. Thousands more operate unofficially.

By the time Zia died in a mysterious 1988 plane crash, the Islamization of Pakistan was well under way. The following year, the Soviet Union, preoccupied with its own implosion, pulled its demoralized troops from Afghanistan. The U.S. promptly declared victory and returned home, leaving the Afghan people to the chaotic rule of the mujahideen warlords. One crucial chapter in the story of radical Islam's ascendancy had come to a close. The one we are still living had just begun. Osama bin Laden and other leaders of the Afghan jihad now moved freely in and out of northwestern Pakistan and its Federally Administered Tribal Areas. The madrassas swelled with the children of the Zia Generation. In the rugged mountainous land shared by Afghanistan and Pakistan, the seeds of the Taliban, and al Qaeda, had been sown.